Understanding molecular adsorption in microporous materials is key to advancing gas separation, storage, and catalysis. Here, we study CO₂ and CH₄ adsorption in crystalline metal–organic frameworks (IRMOF-1, 8, 10, and 14), emphasizing the emergence of metastable states. Molecular simulations reveal that adsorption is governed by a fine balance between fluid–fluid and fluid–framework interactions, leading to transitions between low- and high-density pore-filling states. These metastable features are highly sensitive to pore geometry and thermodynamic conditions, especially near the adsorbate’s triple point. In contrast, water adsorption displays more complex behavior: strong hydrogen bonding induces stable clusters, multiple free energy minima, and exceptionally slow equilibration. These features often escape conventional simulations. Our results underscore the importance of metastability in accurately modeling and designing advanced nanoporous materials for practical applications.